plot_PVCA.df {proBatch} | R Documentation

## plot PVCA, when the analysis is completed

### Description

plot PVCA, when the analysis is completed

### Usage

    plot_PVCA.df(
      pvca_res,
      colors_for_bars = NULL,
      filename = NULL,
      width = NA,
      height = NA,
      units = c("cm", "in", "mm"),
      plot_title = NULL,
      theme = "classic"
    )

### Arguments

`pvca_res` | data frame of weights of Principal Variance Components, result of `calculate_PVCA`
`colors_for_bars` | four-item color vector, specifying colors for the following categories: c('residual', 'biological', 'biol:techn', 'technical')
`filename` | path where the results are saved. If null the object is returned to the active window; otherwise, the object is save into the file. Currently only pdf and png format is supported
`width` | option determining the output image width
`height` | option determining the output image width
`units` | units: 'cm', 'in' or 'mm'
`plot_title` | title of the plot (e.g., processing step + representation level (fragments, transitions, proteins) + purpose (meanplot/corrplot etc))
`theme` | ggplot theme, by default `classic`. Can be easily overriden

### Value

`ggplot` object with bars as weights, colored by bio/tech factors

### Examples

    matrix_test <- example_proteome_matrix[1:150, ]
    pvca_df_res <- prepare_PVCA_df(matrix_test, example_sample_annotation,
    technical_factors = c('MS_batch', 'digestion_batch'),
    biological_factors = c("Diet", "Sex", "Strain"),
    pca_threshold = .6, variance_threshold = .01, fill_the_missing = -1)
    colors_for_bars = c('grey', 'green','blue','red')
    names(colors_for_bars) = c('residual', 'biological','biol:techn','technical')

    pvca_plot <- plot_PVCA.df(pvca_df_res, colors_for_bars)

[Package proBatch version 1.6.0 Index]